[gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:
> Thanks Justin
> 
> I'll try to do that things.
> 
> Some addition questions
> 
> 1) About nvt and apt equilibration
> 
> As I understood ref_t of the system  must be equal to temperature of the 
> phase transition of the specific LIPID.
> But in the npt and nvt.mdp files there are severl enties for ref_t ( for 
> some system groups in index.ndx )
> For my system composed of protein dmpc and water :
> 
>     ref_t   = 323     297    323            ;
> 
> Does all this values in mdp file must be equal ( to the temperature of 
> the lipid  phase transition)
> ref_t   = 297     297    297
>  
>  or each value must correspond to the temperature of phase transition of 
> the individual element ?
>     ref_t   = 323     297    323            ;
> 
> Does thic correct for both NPT and NVT ensembles ?
> 

It is incorrect to set different groups at different temperatures.  Whatever 
result you obtain would be completely unrealistic.

-Justin

> 
> James
> 
> 2011/11/11 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     James Starlight wrote:
> 
>         Justin,
> 
>         Could you tell me what difference in inflategro parameters (
>         cut-off for lipid removing and scaling factors) should I make
>         for insertion protein in another bilayes in comparison tu tutorial ?
> 
> 
>     I've never made any changes; it's always worked just fine.
> 
> 
>         Now I'm working with DMPC. I've inserted symmetrical alpha
>         helices protein in this bilayer but inflategro deleate 2 lipid
>         from upper and just 1  from lower layer. It's strange because I
>         suppose that equal bilayer molecules would be removed :o
> 
> 
>     The number of lipids that are removed will depend on the starting
>     configuration of the membrane and thus where lipids are relative to
>     the protein. Theoretically, a symmetrical protein should delete an
>     equal number of lipids from each leaflet, if the geometry of the top
>     and bottom leaflets is comparable.  Either try placing the protein
>     at a different location to achieve equivalent removal or manually
>     delete a lipid and be sure to equilibrate adequately.
> 
> 
> 
>         On Inflategro's sites I havenot found such specifity for above
>         parameters for different bilayers :(
> 
> 
>     The cutoffs specified are simple grid search parameters.  They do
>     not necessarily need to be altered depending upon the lipid type.
> 
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/__mailman/listinfo/gmx-users
>     <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>     Please search the archive at
>     http://www.gromacs.org/__Support/Mailing_Lists/Search
>     <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>     <http://www.gromacs.org/Support/Mailing_Lists>
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================